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Task #4114 (closed)

Opened 10 years ago

Closed 7 years ago

Better support for N-dimensional data

Reported by: crueden-x Owned by: mhiner-x
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: 4.4.8
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by crueden-x)

Eliminate IFormatReader.getChannelDimTypes and IFormatReader.getChannelDimLengths, in favor of more comprehensive getDimTypes and getDimLengths methods, which return all used dimensions in correct rasterization order.

  • OME dimensions include: X, Y, Z, C, T
  • Examples of non-OME dimensions:
    • lifetime bins
    • excitation wavelength
    • polarization
    • screen
    • plate
    • well
    • field


  • fully capable of expressing N-dimensional image data
  • allows for XZ scans and other spatial configurations
  • eliminates the need for DimensionOrder? and Interleaved core metadata

Work to do:

  1. Rework ChannelSeparator? a little
    • It should always "pull" XY to the front
  1. Rework DimensionSwapper?; it is more complex now
  1. Rework DataBrowser? to use new methods, displaying extra sliders as before
  1. Rework FileStitcher? and AxisGuesser? a bit
    • Guessed axes become new dimensions
  1. Change anywhere else that calls getChannelDim* methods
  1. InCell? reader can be retrofitted to use this new functionality
    • Certain other readers can benefit as well: Flex, Fluoview, ...
  1. Initially, conversion to OME-TIFF with bfconvert should throw an exception if any dimensions beyond 5D exist, since there is nowhere in the OME-XML schema to store the extra dimensional information

Change History (4)

comment:1 Changed 10 years ago by jmoore

imported from bio-formats:#398

comment:2 Changed 10 years ago by crueden-x

  • Description modified (diff)
  • Owner changed from curtis to crueden-x
  • Reporter changed from curtis to crueden-x

comment:3 Changed 9 years ago by crueden-x

  • Milestone changed from OMERO-Beta4.4 to Unscheduled
  • Owner changed from crueden-x to mhiner-x

This work fits in well with our SCIFIO efforts. Added to SCIFIO core refactoring story.

comment:4 Changed 7 years ago by mhiner-x

  • Resolution set to duplicate
  • Status changed from new to closed
  • Version set to 4.4.8

Moved to github under SCIFIO issues.

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